Rdisop 1.46.0
Steffen Neumann
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/Rdisop |
| Branch: RELEASE_3_10 |
| Last Commit: fdd73a9 |
| Last Changed Date: 2019-10-29 13:07:53 -0400 (Tue, 29 Oct 2019) |
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | |
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/Rdisop_1.46.0.tar.gz && rm -rf Rdisop.buildbin-libdir && mkdir Rdisop.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rdisop.buildbin-libdir Rdisop_1.46.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL Rdisop_1.46.0.zip && rm Rdisop_1.46.0.tar.gz Rdisop_1.46.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 683k 100 683k 0 0 11.1M 0 --:--:-- --:--:-- --:--:-- 11.9M
install for i386
* installing *source* package 'Rdisop' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c disop.cpp -o disop.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
from disop.cpp:18:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
^
In file included from disop.cpp:28:0:
./imslib/src/ims/decomp/decomputils.h: In function 'std::pair<typename DecompositionWeights::alphabet_mass_type, typename DecompositionWeights::alphabet_mass_type> ims::DecompUtils::getMinMaxWeightsRoundingErrors(const DecompositionWeights&)':
./imslib/src/ims/decomp/decomputils.h:92:53: warning: typedef 'weight_type' locally defined but not used [-Wunused-local-typedefs]
typedef typename DecompositionWeights::weight_type weight_type;
^
disop.cpp: In function 'bool isValidMyNitrogenRule(const ims::ComposedElement&, int)':
disop.cpp:106:8: warning: unused variable 'parityeven' [-Wunused-variable]
bool parityeven = !parityodd;
^
disop.cpp: In function 'SEXPREC* decomposeIsotopes(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
disop.cpp:228:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
^
disop.cpp:231:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
^
disop.cpp:239:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) {
^
disop.cpp:239:68: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) {
^
disop.cpp:191:6: warning: unused variable 'number_molecules_shown' [-Wunused-variable]
int number_molecules_shown = 100;
^
disop.cpp:169:39: warning: typedef 'mass_type' locally defined but not used [-Wunused-local-typedefs]
typedef distribution_t::mass_type mass_type;
^
disop.cpp:171:47: warning: typedef 'nominal_mass_type' locally defined but not used [-Wunused-local-typedefs]
typedef distribution_t::nominal_mass_type nominal_mass_type;
^
disop.cpp:174:42: warning: typedef 'decomposition_type' locally defined but not used [-Wunused-local-typedefs]
typedef decompositions_t::value_type decomposition_type;
^
disop.cpp: In function 'SEXPREC* calculateScore(SEXP, SEXP, SEXP, SEXP)':
disop.cpp:390:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
^
disop.cpp:390:68: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
^
disop.cpp:407:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
^
disop.cpp:410:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
^
disop.cpp:414:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
^
disop.cpp:414:68: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
^
disop.cpp:377:40: warning: typedef 'mass_type' locally defined but not used [-Wunused-local-typedefs]
typedef distribution_t::mass_type mass_type;
^
disop.cpp: In function 'SEXPREC* rlistScores(std::multimap<score_type, ims::ComposedElement, std::greater<score_type> >, int)':
disop.cpp:626:43: warning: typedef 'scorer_type' locally defined but not used [-Wunused-local-typedefs]
typedef DistributionProbabilityScorer scorer_type;
^
disop.cpp: In function 'void initializeCHNOPS(alphabet_t&, int)':
disop.cpp:709:32: warning: typedef 'elements_type' locally defined but not used [-Wunused-local-typedefs]
typedef alphabet_t::container elements_type;
^
disop.cpp: In function 'void initializeAlphabet(SEXP, alphabet_t&, int)':
disop.cpp:814:33: warning: typedef 'elements_type' locally defined but not used [-Wunused-local-typedefs]
typedef alphabet_t::container elements_type;
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/element.cpp -o imslib/src/ims/element.o
In file included from imslib/src/ims/element.cpp:6:0:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/composedelement.cpp -o imslib/src/ims/composedelement.o
In file included from ./imslib/src/ims/composedelement.h:7:0,
from imslib/src/ims/composedelement.cpp:8:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
^
imslib/src/ims/composedelement.cpp: In constructor 'ims::ComposedElement::ComposedElement(const name_type&, const ims::Alphabet&, unsigned int)':
imslib/src/ims/composedelement.cpp:28:82: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
parser = std::auto_ptr<sequence_parser_type>(new StandardMoleculeSequenceParser);
^
imslib/src/ims/composedelement.cpp:30:74: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
parser = std::auto_ptr<sequence_parser_type>(new MoleculeSequenceParser);
^
imslib/src/ims/composedelement.cpp: At global scope:
imslib/src/ims/composedelement.cpp:116:110: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
void ComposedElement::initializeElements(const Alphabet& alphabet, std::auto_ptr<sequence_parser_type> parser)
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/alphabet.cpp -o imslib/src/ims/alphabet.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
from imslib/src/ims/alphabet.cpp:6:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/distributedalphabet.cpp -o imslib/src/ims/distributedalphabet.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
from ./imslib/src/ims/distributedalphabet.h:7,
from imslib/src/ims/distributedalphabet.cpp:7:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/base/parser/keggligandcompoundsparser.cpp -o imslib/src/ims/base/parser/keggligandcompoundsparser.o
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp: In member function 'virtual void ims::KeggLigandCompoundsParser::parse(const sequence_type&)':
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp:53:31: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
for (; letter_pos < last_pos &&
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/calib/matchmatrix.cpp -o imslib/src/ims/calib/matchmatrix.o
imslib/src/ims/calib/matchmatrix.cpp: In member function 'std::auto_ptr<std::map<int, int> > ims::MatchMatrix::countMatches()':
imslib/src/ims/calib/matchmatrix.cpp:82:37: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
std::auto_ptr<std::map<int,int> > m(new std::map<int,int>);
^
imslib/src/ims/calib/matchmatrix.cpp: At global scope:
imslib/src/ims/calib/matchmatrix.cpp:102:72: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
std::auto_ptr<std::map<int,int> > MatchMatrix::countMatchesRestrictive() {
^
imslib/src/ims/calib/matchmatrix.cpp: In member function 'std::auto_ptr<std::map<int, int> > ims::MatchMatrix::countMatchesRestrictive()':
imslib/src/ims/calib/matchmatrix.cpp:103:37: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
std::auto_ptr<std::map<int,int> > m(new std::map<int,int>);
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/calib/linearpointsetmatcher.cpp -o imslib/src/ims/calib/linearpointsetmatcher.o
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:0:
./imslib/src/ims/calib/linearpointsetmatcher.h: In member function 'void ims::LinearPointSetMatcher::countMatchesOneToOne(RandomAccessIterator, RandomAccessIterator, RandomAccessIterator, RandomAccessIterator, const std::vector<ims::RepresentativeScale>&, int, int, float)':
./imslib/src/ims/calib/linearpointsetmatcher.h:281:44: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
std::auto_ptr<std::map<int,int> > mapping(0);
^
./imslib/src/ims/calib/linearpointsetmatcher.h: In member function 'int ims::LinearPointSetMatcher::match(RandomAccessIterator, RandomAccessIterator, RandomAccessIterator, RandomAccessIterator)':
./imslib/src/ims/calib/linearpointsetmatcher.h:324:76: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
results.mapping = std::auto_ptr<std::map<int,int> >(new std::map<int,int>);
^
./imslib/src/ims/calib/linearpointsetmatcher.h:326:56: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
results.mapping = std::auto_ptr<std::map<int,int> >(0);
^
imslib/src/ims/calib/linearpointsetmatcher.cpp: At global scope:
imslib/src/ims/calib/linearpointsetmatcher.cpp:84:71: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
std::auto_ptr<std::map<int,int> > LinearPointSetMatcher::getMapping() const {
^
imslib/src/ims/calib/linearpointsetmatcher.cpp: In member function 'std::auto_ptr<std::map<int, int> > ims::LinearPointSetMatcher::getMapping() const':
imslib/src/ims/calib/linearpointsetmatcher.cpp:86:45: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
return std::auto_ptr<std::map<int,int> >(0); // TODO throw sth. instead
^
imslib/src/ims/calib/linearpointsetmatcher.cpp:89:85: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
return std::auto_ptr<std::map<int,int> >(new std::map<int,int>(*(results.mapping)));
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/decomp/realmassdecomposer.cpp -o imslib/src/ims/decomp/realmassdecomposer.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
from ./imslib/src/ims/decomp/decomputils.h:12,
from imslib/src/ims/decomp/realmassdecomposer.cpp:9:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
^
In file included from imslib/src/ims/decomp/realmassdecomposer.cpp:9:0:
./imslib/src/ims/decomp/decomputils.h: In function 'std::pair<typename DecompositionWeights::alphabet_mass_type, typename DecompositionWeights::alphabet_mass_type> ims::DecompUtils::getMinMaxWeightsRoundingErrors(const DecompositionWeights&)':
./imslib/src/ims/decomp/decomputils.h:92:53: warning: typedef 'weight_type' locally defined but not used [-Wunused-local-typedefs]
typedef typename DecompositionWeights::weight_type weight_type;
^
imslib/src/ims/decomp/realmassdecomposer.cpp: In constructor 'ims::RealMassDecomposer::RealMassDecomposer(const ims::Weights&)':
imslib/src/ims/decomp/realmassdecomposer.cpp:22:44: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
new integer_decomposer_type(weights));
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/characteralphabet.cpp -o imslib/src/ims/characteralphabet.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
from ./imslib/src/ims/characteralphabet.h:6,
from imslib/src/ims/characteralphabet.cpp:3:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/nitrogenrulefilter.cpp -o imslib/src/ims/nitrogenrulefilter.o
In file included from ./imslib/src/ims/composedelement.h:7:0,
from ./imslib/src/ims/nitrogenrulefilter.h:4,
from imslib/src/ims/nitrogenrulefilter.cpp:5:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o Rdisop.dll tmp.def disop.o imslib/src/ims/element.o imslib/src/ims/composedelement.o imslib/src/ims/isotopedistribution.o imslib/src/ims/alphabet.o imslib/src/ims/weights.o imslib/src/ims/distributedalphabet.o imslib/src/ims/transformation.o imslib/src/ims/isotopespecies.o imslib/src/ims/base/parser/alphabettextparser.o imslib/src/ims/base/parser/distributedalphabettextparser.o imslib/src/ims/base/parser/massestextparser.o imslib/src/ims/base/parser/moleculesequenceparser.o imslib/src/ims/base/parser/standardmoleculesequenceparser.o imslib/src/ims/base/parser/keggligandcompoundsparser.o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o imslib/src/ims/calib/linepairstabber.o imslib/src/ims/calib/matchmatrix.o imslib/src/ims/calib/linearpointsetmatcher.o imslib/src/ims/decomp/realmassdecomposer.o imslib/src/ims/utils/distribution.o imslib/src/ims/distributionprobabilityscorer.o imslib/src/ims/characteralphabet.o imslib/src/ims/nitrogenrulefilter.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/Rdisop.buildbin-libdir/00LOCK-Rdisop/00new/Rdisop/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Rdisop'
finding HTML links ... done
addMolecules html
decomposeMass html
getMolecule html
initializeCHNOPS html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'Rdisop' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c disop.cpp -o disop.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
from disop.cpp:18:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
^
In file included from disop.cpp:28:0:
./imslib/src/ims/decomp/decomputils.h: In function 'std::pair<typename DecompositionWeights::alphabet_mass_type, typename DecompositionWeights::alphabet_mass_type> ims::DecompUtils::getMinMaxWeightsRoundingErrors(const DecompositionWeights&)':
./imslib/src/ims/decomp/decomputils.h:92:53: warning: typedef 'weight_type' locally defined but not used [-Wunused-local-typedefs]
typedef typename DecompositionWeights::weight_type weight_type;
^
disop.cpp: In function 'bool isValidMyNitrogenRule(const ims::ComposedElement&, int)':
disop.cpp:106:8: warning: unused variable 'parityeven' [-Wunused-variable]
bool parityeven = !parityodd;
^
disop.cpp: In function 'SEXPREC* decomposeIsotopes(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
disop.cpp:228:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
^
disop.cpp:231:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
^
disop.cpp:239:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) {
^
disop.cpp:239:68: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) {
^
disop.cpp:191:6: warning: unused variable 'number_molecules_shown' [-Wunused-variable]
int number_molecules_shown = 100;
^
disop.cpp:169:39: warning: typedef 'mass_type' locally defined but not used [-Wunused-local-typedefs]
typedef distribution_t::mass_type mass_type;
^
disop.cpp:171:47: warning: typedef 'nominal_mass_type' locally defined but not used [-Wunused-local-typedefs]
typedef distribution_t::nominal_mass_type nominal_mass_type;
^
disop.cpp:174:42: warning: typedef 'decomposition_type' locally defined but not used [-Wunused-local-typedefs]
typedef decompositions_t::value_type decomposition_type;
^
disop.cpp: In function 'SEXPREC* calculateScore(SEXP, SEXP, SEXP, SEXP)':
disop.cpp:390:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
^
disop.cpp:390:68: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
^
disop.cpp:407:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
^
disop.cpp:410:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
^
disop.cpp:414:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
^
disop.cpp:414:68: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
^
disop.cpp:377:40: warning: typedef 'mass_type' locally defined but not used [-Wunused-local-typedefs]
typedef distribution_t::mass_type mass_type;
^
disop.cpp: In function 'SEXPREC* rlistScores(std::multimap<score_type, ims::ComposedElement, std::greater<score_type> >, int)':
disop.cpp:626:43: warning: typedef 'scorer_type' locally defined but not used [-Wunused-local-typedefs]
typedef DistributionProbabilityScorer scorer_type;
^
disop.cpp: In function 'void initializeCHNOPS(alphabet_t&, int)':
disop.cpp:709:32: warning: typedef 'elements_type' locally defined but not used [-Wunused-local-typedefs]
typedef alphabet_t::container elements_type;
^
disop.cpp: In function 'void initializeAlphabet(SEXP, alphabet_t&, int)':
disop.cpp:814:33: warning: typedef 'elements_type' locally defined but not used [-Wunused-local-typedefs]
typedef alphabet_t::container elements_type;
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/element.cpp -o imslib/src/ims/element.o
In file included from imslib/src/ims/element.cpp:6:0:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/composedelement.cpp -o imslib/src/ims/composedelement.o
In file included from ./imslib/src/ims/composedelement.h:7:0,
from imslib/src/ims/composedelement.cpp:8:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
^
imslib/src/ims/composedelement.cpp: In constructor 'ims::ComposedElement::ComposedElement(const name_type&, const ims::Alphabet&, unsigned int)':
imslib/src/ims/composedelement.cpp:28:82: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
parser = std::auto_ptr<sequence_parser_type>(new StandardMoleculeSequenceParser);
^
imslib/src/ims/composedelement.cpp:30:74: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
parser = std::auto_ptr<sequence_parser_type>(new MoleculeSequenceParser);
^
imslib/src/ims/composedelement.cpp: At global scope:
imslib/src/ims/composedelement.cpp:116:110: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
void ComposedElement::initializeElements(const Alphabet& alphabet, std::auto_ptr<sequence_parser_type> parser)
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/alphabet.cpp -o imslib/src/ims/alphabet.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
from imslib/src/ims/alphabet.cpp:6:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/distributedalphabet.cpp -o imslib/src/ims/distributedalphabet.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
from ./imslib/src/ims/distributedalphabet.h:7,
from imslib/src/ims/distributedalphabet.cpp:7:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/base/parser/keggligandcompoundsparser.cpp -o imslib/src/ims/base/parser/keggligandcompoundsparser.o
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp: In member function 'virtual void ims::KeggLigandCompoundsParser::parse(const sequence_type&)':
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp:53:31: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
for (; letter_pos < last_pos &&
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/calib/matchmatrix.cpp -o imslib/src/ims/calib/matchmatrix.o
imslib/src/ims/calib/matchmatrix.cpp: In member function 'std::auto_ptr<std::map<int, int> > ims::MatchMatrix::countMatches()':
imslib/src/ims/calib/matchmatrix.cpp:82:37: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
std::auto_ptr<std::map<int,int> > m(new std::map<int,int>);
^
imslib/src/ims/calib/matchmatrix.cpp: At global scope:
imslib/src/ims/calib/matchmatrix.cpp:102:72: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
std::auto_ptr<std::map<int,int> > MatchMatrix::countMatchesRestrictive() {
^
imslib/src/ims/calib/matchmatrix.cpp: In member function 'std::auto_ptr<std::map<int, int> > ims::MatchMatrix::countMatchesRestrictive()':
imslib/src/ims/calib/matchmatrix.cpp:103:37: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
std::auto_ptr<std::map<int,int> > m(new std::map<int,int>);
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/calib/linearpointsetmatcher.cpp -o imslib/src/ims/calib/linearpointsetmatcher.o
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:0:
./imslib/src/ims/calib/linearpointsetmatcher.h: In member function 'void ims::LinearPointSetMatcher::countMatchesOneToOne(RandomAccessIterator, RandomAccessIterator, RandomAccessIterator, RandomAccessIterator, const std::vector<ims::RepresentativeScale>&, int, int, float)':
./imslib/src/ims/calib/linearpointsetmatcher.h:281:44: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
std::auto_ptr<std::map<int,int> > mapping(0);
^
./imslib/src/ims/calib/linearpointsetmatcher.h: In member function 'int ims::LinearPointSetMatcher::match(RandomAccessIterator, RandomAccessIterator, RandomAccessIterator, RandomAccessIterator)':
./imslib/src/ims/calib/linearpointsetmatcher.h:324:76: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
results.mapping = std::auto_ptr<std::map<int,int> >(new std::map<int,int>);
^
./imslib/src/ims/calib/linearpointsetmatcher.h:326:56: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
results.mapping = std::auto_ptr<std::map<int,int> >(0);
^
imslib/src/ims/calib/linearpointsetmatcher.cpp: At global scope:
imslib/src/ims/calib/linearpointsetmatcher.cpp:84:71: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
std::auto_ptr<std::map<int,int> > LinearPointSetMatcher::getMapping() const {
^
imslib/src/ims/calib/linearpointsetmatcher.cpp: In member function 'std::auto_ptr<std::map<int, int> > ims::LinearPointSetMatcher::getMapping() const':
imslib/src/ims/calib/linearpointsetmatcher.cpp:86:45: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
return std::auto_ptr<std::map<int,int> >(0); // TODO throw sth. instead
^
imslib/src/ims/calib/linearpointsetmatcher.cpp:89:85: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
return std::auto_ptr<std::map<int,int> >(new std::map<int,int>(*(results.mapping)));
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/decomp/realmassdecomposer.cpp -o imslib/src/ims/decomp/realmassdecomposer.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
from ./imslib/src/ims/decomp/decomputils.h:12,
from imslib/src/ims/decomp/realmassdecomposer.cpp:9:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
^
In file included from imslib/src/ims/decomp/realmassdecomposer.cpp:9:0:
./imslib/src/ims/decomp/decomputils.h: In function 'std::pair<typename DecompositionWeights::alphabet_mass_type, typename DecompositionWeights::alphabet_mass_type> ims::DecompUtils::getMinMaxWeightsRoundingErrors(const DecompositionWeights&)':
./imslib/src/ims/decomp/decomputils.h:92:53: warning: typedef 'weight_type' locally defined but not used [-Wunused-local-typedefs]
typedef typename DecompositionWeights::weight_type weight_type;
^
imslib/src/ims/decomp/realmassdecomposer.cpp: In constructor 'ims::RealMassDecomposer::RealMassDecomposer(const ims::Weights&)':
imslib/src/ims/decomp/realmassdecomposer.cpp:22:44: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
new integer_decomposer_type(weights));
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/characteralphabet.cpp -o imslib/src/ims/characteralphabet.o
In file included from ./imslib/src/ims/alphabet.h:8:0,
from ./imslib/src/ims/characteralphabet.h:6,
from imslib/src/ims/characteralphabet.cpp:3:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -I./imslib/src/ -O2 -Wall -mtune=core2 -c imslib/src/ims/nitrogenrulefilter.cpp -o imslib/src/ims/nitrogenrulefilter.o
In file included from ./imslib/src/ims/composedelement.h:7:0,
from ./imslib/src/ims/nitrogenrulefilter.h:4,
from imslib/src/ims/nitrogenrulefilter.cpp:5:
./imslib/src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./imslib/src/ims/element.h:166:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < IsotopeDistribution::SIZE; i++) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o Rdisop.dll tmp.def disop.o imslib/src/ims/element.o imslib/src/ims/composedelement.o imslib/src/ims/isotopedistribution.o imslib/src/ims/alphabet.o imslib/src/ims/weights.o imslib/src/ims/distributedalphabet.o imslib/src/ims/transformation.o imslib/src/ims/isotopespecies.o imslib/src/ims/base/parser/alphabettextparser.o imslib/src/ims/base/parser/distributedalphabettextparser.o imslib/src/ims/base/parser/massestextparser.o imslib/src/ims/base/parser/moleculesequenceparser.o imslib/src/ims/base/parser/standardmoleculesequenceparser.o imslib/src/ims/base/parser/keggligandcompoundsparser.o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o imslib/src/ims/calib/linepairstabber.o imslib/src/ims/calib/matchmatrix.o imslib/src/ims/calib/linearpointsetmatcher.o imslib/src/ims/decomp/realmassdecomposer.o imslib/src/ims/utils/distribution.o imslib/src/ims/distributionprobabilityscorer.o imslib/src/ims/characteralphabet.o imslib/src/ims/nitrogenrulefilter.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/Rdisop.buildbin-libdir/Rdisop/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rdisop' as Rdisop_1.46.0.zip
* DONE (Rdisop)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'Rdisop' successfully unpacked and MD5 sums checked